Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin

Both human and bovine prothrombin fragment 2 (the second kringle) have been cocrystallized separately with human PPACK (D-Phe-Pro-Arg)-thrombin, and the structures of these noncovalent complexes have been determined and refined (R = 0.155 and 0.157, respectively) at 3.3-Å resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogens K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg70Asp substitution, but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix, and the hairpin β-turn of the second inner loop pivots at Val64 and Asp70 by 60°. Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating any vestige of the cationic center of the lysine binding site. Since fragment 2 has not been reported to bind lysine, it most likely has a different inherent folding conformation for the second outer loop, as has also been observed to be the case with TPA K2 and the urokinase kringle. The movement of the Val64-Asp70 β-turn is most likely a conformational change accompanying complexation, which reveals a new heretofore unsuspected flexibility in kringles. The fragment 2-thrombin complex is only the second cassette module-catalytic domain structure to be determined for a multidomain blood protein and only the third domain-domain interaction to be described among such proteins, the others being factor Xa without a Gla domain and Ca2+ prothrombin fragment 1 with a Gla domain and a kringle. © 1993 American Chemical Society.

Synthesis, characterization and molecular structures of the pyridinium trans-bis(pyridine)tetrachlororuthenate(III) and pyridinium trans-(carbonyl)(pyridine)tetrachlororuthenate(III)

The pyH[trans-RuCl4(py)2](1) and pyH[trans-RuCl4(CO)(py)](2) complexes were synthesized and found to crystallize in space group P21/n, Z = 4 with a = 8.080(7), b = 22.503(7), c = 10.125(6) Å, β = 93.19(6)° for (1) and a = 7.821(1), b = 10.337(3), c = 19.763(3) Å, β = 93.07(1)° for (2). The structures were solved by Patterson and difference Fourier techniques and refined to R = 0.062 for (1) and R = 0.038 for (2). In both cases the Ru(III) ion is octahedrally coordinated to four co-planar chlorine atoms, the nitrogen of the pyridine rings or carbon from the carbon monoxide. Another protonated pyridine group, which forms the counter-cation completes the crystal structures. The UV-Vis absorption spectra show three bands: (1) 360 (ε = 1180 M-1 cm-1), 441 (ε = 3200 M-1 cm-1) and 532 nm (ε = 400 M-1 cm-1); (2) 315(ε = 1150 M-1 cm-1), 442 (ε = 3170 M-1 cm-1) and 530 nm (ε = 390 M-1 cm-1). The two higher energy bands were associated with ligand-to-metal charge transfer transitions and a third band at lower energy was assigned to a d-d transition. Low temperature EPR data confirmed the presence of the paramagnetically active Ru(III) and it is consistent with axial symmetry of the complexes. The position of the stretching CO band in complex (2) is discussed in terms of metal-CO backbonding.

Synthesis and characterization of the mer-[RuCl3(NO)(dppb)] isomer. X-ray structures of fac-[RuCl3(NO)(dppm)], cis-[RuCl2(dppm)2] and mer-[RuCl3(NO)(dppb)] [dppm=1,2-Bis(diphenylphosphino)methane and dppb=1,4-Bis(diphenylphosphino)butane]

The fac-[RuCl3(NO)(dppm)] (1) and cis-[RuCl2(dppm)2] (2) complexes were obtained with co-crystallization in the solid state from the reaction of RuCl3(NO) with the diphosphine in dichloromethane. mer-[RuCl3(NO)(dppb)] (3) was obtained from [RuCl3(dppb)(H2O)] by bubbling NO for 30 min in the same solvent. The crystal and molecular structures of these three compounds have been determined from X-ray studies. © Elsevier Science Ltd.

Crystal and supramolecular structures of dysprosium(III) 2-methoxybenzoate tetrahydrate

The compound dysprosium(III) 2-metoxybenzoate, {[Dy(2-MeO-Bz)2μ-(2-MeO-Bz)(H2O)2]2·4H2O}n (2-MeO-Bz = 2- methoxybenzoate), was synthesized from a reaction mixture containing DyCl3 and Na(2-MeO-Bz), and characterized by single-crystal X-ray diffraction. The molecular structure showed dinuclear units in which each Dy(III) ion is coordinated by nine oxygen atoms. The carboxylato groups are bound to the dysprosium centers in two modes: bidentate chelating and tridentate chelating-bridging. Besides this, the occurrence of hydrogen bonds involving a coordinated water molecule and carboxylato groups leads to the formation of helicoidal chains along the crystal lattice, resulting in a supramolecular one-dimensional polymer. 2008 © The Japan Society for Analytical Chemistry.

Unbiased approach to diagnose the nutrient status of red guava (Psidium guajava)

Fertilization of guava relies on soil and tissue testing. The interpretation of tissue test is currently conducted by comparing nutrient concentrations or dual ratios with critical values or ranges. The critical value approach is affected by nutrient interactions. Nutrient interactions can be described by dual ratios where two nutrients are compressed into a single expression or a ternary diagrams where one redundant proportion can be computed by difference between 100% and the sum of the other two. There are D(D-1) possible dual ratios in a D-parts composition and most of them are thus redundant. Nutrients are components of a mixture that convey relative, not absolute information on the composition. There are D-1 balances between components or ingredients in any mixture. Compositional data are intrinsically redundant, scale dependent and non-normally distributed. Based on the principles of equilibrium and orthogonality, the nutrient balance concept projects D-1 isometric log ratio (ilr) coordinates into the Euclidean space. The D-1 balances between groups of nutrients are ordered to reflect knowledge in plant physiology, soil fertility and crop management. Our objective was to evaluate the ilr approach using nutrient data from a guava orchard survey and fertilizer trials across the state of São Paulo, Brazil. Cationic balances varied widely between orchards. We found that the Redfield N/P ratio of 13 was critical for high guava yield. We present guava yield maps in ternary diagrams. Although the ratio between nutrients changing in the same direction with time is often assumed to be stationary, most guava nutrient balances and dual ratios were found to be non-stationary. The ilr model provided an unbiased nutrient diagnosis of guava. © ISHS.

First crystal structures of lanthanide-hydrocinnamate complexes: Hydrothermal synthesis and photophysical studies

Five new lanthanide(III) complexes of hydrocinnamic acid (Hcin), [Ln(cin)3(H2O)3]·3Hcin (Ln = Tb(III) (1), Dy(III) (2), Er(III) (3), Eu(III) (4) and Gd(III) (5)) have been synthesized and characterized. The X-ray structures of 1-5 reveal that all compounds are isostructural and that each lanthanide ion is nine-coordinated by oxygen atoms in an overall distorted tricapped trigonal-prismatic geometry. Six oxygen atoms are provided by carboxylate moieties, and the other three by water molecules. The supramolecular architectures of 1-5 show the presence of uncoordinated hydrocinnamic acid molecules which induce the formation of numerous hydrogen bonds. The photophysical properties of these complexes in the solid state at room temperature were studied using diffuse reflectance (DR), fluorescence excitation and emission spectra. An energy level diagram was used to establish the most relevant channels involved in the ligand-to-metal energy transfer, indicating that cin- ligands can act as intramolecular energy donors for Tb(III), Dy(III) and Eu(III) ions. © 2012 Elsevier B.V.

Simple procedure for nutrient analysis of coffee plant with energy dispersive X-ray fluorescence spectrometry (EDXRF)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural bases for a complete myotoxic mechanism: Crystal structures of two non-catalytic phospholipases A(2)-like from Bothrops brazili venom

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Long-range and short-range structures of cube-like shape SrTiO3 powders: microwave-assisted hydrothermal synthesis and photocatalytic activity

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Soil and leaf nutrient content of tree species support deciduous forests on limestone outcrops as a eutrophic ecosystem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Theoretical study of molecular and electronic structures of 5(1) knot systems: two-layered ONIOM calculations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chemical composition of essential oils from the vegetative and reproductive structures of Copaifera langsdorffii Desf

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Antimicrobial resistance of heterotrophic marine bacteria isolated from seawater and sands of recreational beaches with different organic pollution levels in southeastern Brazil: evidences of resistance dissemination

Antimicrobial resistance of marine heterotrophic bacteria to different antimicrobials agents were evaluated in seawater, dry and wet sands from three marine recreational beaches with different pollution levels. In all studied beaches, the greatest frequencies of resistance were found in relation to penicillin. on Gonzaguinha, the most polluted beach, 72.3% of all isolated strains showed simple resistance, whilst 8.33% had multiple resistance. The values found on Ilha Porchat beach, were 70.8% and 6.9% for simple and multiple resistances, respectively. on GuaraA(0), the less polluted beach, only 35.3% of isolated strains had simple resistance. Multiple resistance was not observed. While samples from Gonzaguinha and Ilha Porchat beach showed isolated strains resistant to seven and six different antimicrobial agents, respectively, samples from GuaraA(0) beach were resistant only to penicillin and erytromicin. The positive correlations obtained between the degree of seawater contamination and frequency and variability of bacterial resistance indicate that polluted marine recreational waters and sands are sources of resistant bacteria contributing thus, to the dissemination of bacterial resistance.

Digestibility and metabolizable energy of maize gluten feed for dogs as measured by two different techniques

Maize gluten feed (MGF) is a co-product of wet milling of maize, and is composed of structures that remain after most starch, gluten and germ has been extracted from the grain. Although currently used in dog foods, its digestibility and energy values have not been documented. Two techniques were used to determine nutrient digestibility of MGF for dog foods. Both techniques used extruded diets fed to Beagle dogs, with six replicates per diet. The first study used a difference method in which 300 g/kg of a reference diet was replaced by MGF. Based on the difference method, the coefficient of total tract apparent digestibility (CTTAD) of MGF was 0.53 for dry matter (DM), 0.69 for crude protein (CP), 0.74 for fat, 0.99 for starch, and 0.55 for gross energy (GE). The calculated metabolizable energy (ME) of MGF was 7.99 MJ/kg (as-fed). The second study used a regression method and included a basal diet and a basal diet with 70, 140 and 210 g MGF/kg of diet (as a substitute for maize starch). Maize gluten feed inclusion resulted in a linear reduction of CTTAD of DM (R(2)=0.99; P<0.001), CP (R(2)=0.95; P=0.002), fat (R(2)=0.87; P=0.009). starch (R(2)=0.81; P<0.001), and GE (R(2)=0.99; P<0.001). Faecal production increased linearly from 56 g to 107 g/dog/d (R(2)=0.99; P<0.001), with a linear reduction of faecal DM (R(2)=0.99: P<0.001) and a linear increase in faecal lactic acid concentration (P<0.02). Both urine (R(2)=0.77; P=0.029) and faeces (R(2)=0.92: P=0.019) showed a linear reduction in pH. Results of ingredient MAD obtained by the regression and difference methods were close (6% or less of variation) for CP, fat, and starch, and also for ME content (1.4% higher for the difference method), but the two methods disagreed on calculated CTTAD of DM and organic matter. The high dietary fiber content of MGF (382 g/kg) may explain the low digestibility of this ingredient. Maize gluten feed could be a useful ingredient for formulations designed to have low energy or reduce the urine pH of dogs. (C) 2011 Elsevier B.V. All rights reserved.